ubic.gemma.web.services.Gene2GoTermEndpoint.java Source code

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Here is the source code for ubic.gemma.web.services.Gene2GoTermEndpoint.java

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/*
 * The Gemma project
 * 
 * Copyright (c) 2008 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */

package ubic.gemma.web.services;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.StopWatch;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import ubic.basecode.ontology.model.OntologyTerm;
import ubic.gemma.core.genome.gene.service.GeneService;
import ubic.gemma.core.ontology.providers.GeneOntologyService;
import ubic.gemma.core.ontology.providers.GeneOntologyServiceImpl;
import ubic.gemma.model.genome.Gene;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;

/**
 * Given a collection of Gene IDs, will return a collection of Gene Ontology URIs for each gene.
 * 
 * @author klc, gavin
 *
 */

public class Gene2GoTermEndpoint extends AbstractGemmaEndpoint {

    private static Log log = LogFactory.getLog(Gene2GoTermEndpoint.class);

    private GeneOntologyService geneOntologyService;

    private GeneService geneService;

    /**
     * The local name of the expected request/response.
     */
    public static final String GENE2GO_LOCAL_NAME = "gene2Go";

    /**
     * Sets the "business service" to delegate to.
     */
    public void setGeneOntologyService(GeneOntologyService goS) {
        this.geneOntologyService = goS;
    }

    public void setGeneService(GeneService geneS) {
        this.geneService = geneS;
    }

    /**
     * Reads the given <code>requestElement</code>, and sends a the response back.
     * 
     * @param requestElement the contents of the SOAP message as DOM elements
     * @param document a DOM document to be used for constructing <code>Node</code>s
     * @return the response element
     */
    @Override
    protected Element invokeInternal(Element requestElement, Document document) {
        StopWatch watch = new StopWatch();
        watch.start();

        setLocalName(GENE2GO_LOCAL_NAME);

        Collection<String> geneResult = getArrayValues(requestElement, "gene_ids");

        log.info("XML input read: " + geneResult.size() + " gene ids");
        // start building the wrapper
        // build xml manually for mapped result rather than use buildWrapper inherited from AbstractGemmeEndpoint
        // log.info( "Building " + GENE2GO_LOCAL_NAME + " XML response" );

        String elementName1 = "gene_id";
        String elementName2 = "goIdList";

        Element responseWrapper = document.createElementNS(NAMESPACE_URI, GENE2GO_LOCAL_NAME);
        Element responseElement = document.createElementNS(NAMESPACE_URI, GENE2GO_LOCAL_NAME + RESPONSE);
        responseWrapper.appendChild(responseElement);

        for (String geneString : geneResult) {

            Long geneId = Long.parseLong(geneString);
            Gene gene = geneService.load(geneId);
            if (gene == null) {
                String msg = "No gene with ids, " + geneId + " can be found.";
                return buildBadResponse(document, msg);
            }

            Collection<OntologyTerm> terms = geneOntologyService.getGOTerms(gene);

            // get the labels and store them
            Collection<String> goTerms = new HashSet<String>();
            if (terms != null) {
                for (OntologyTerm ot : terms) {
                    goTerms.add(GeneOntologyServiceImpl.asRegularGoId(ot));
                }
            } else
                goTerms.add("NaN");
            String elementString1 = geneId.toString();
            String elementString2 = encode(retainNumericIds(goTerms).toArray());

            Element e1 = document.createElement(elementName1);
            e1.appendChild(document.createTextNode(elementString1));
            responseElement.appendChild(e1);

            Element e2 = document.createElement(elementName2);
            e2.appendChild(document.createTextNode(elementString2));
            responseElement.appendChild(e2);
        }
        watch.stop();
        Long time = watch.getTime();
        // log.info( "Finished generating result. Sending response to client." );
        log.info("XML response for GO Term results built in " + time + "ms.");

        return responseWrapper;

    }

    /**
     * @param regularIds - input collection will be unchanged
     * @return - collection of GO ids, without the "GO:" infront, only the numeric portion of the id is returned
     */
    private Collection<String> retainNumericIds(Collection<String> regularIds) {
        Collection<String> numericIds = new ArrayList<String>();
        for (String id : regularIds) {
            numericIds.add(StringUtils.substring(id, 3));
        }
        return numericIds;

    }

}